Nearest Neighbor
Database References

• Turner 1999
  • Watson-Crick Pairs
  • GU Pairs
  • Dangling Ends
  • Terminal Mismatches
  • Hairpin Loops
  • Bulge Loops
  • Internal Loops
  • Multibranch Loops
  • Exterior Loops
• Turner 2004
  • Watson-Crick Pairs
  • GU Pairs
  • Dangling Ends
  • Terminal Mismatches
  • Hairpin Loops
  • Bulge Loops
  • Internal Loops
  • Multibranch Loops
  • Exterior Loops
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This is the set of references to optical melting experiments that have been utilized to develop nearest neighbor parameters for RNA folding free energy and enthalpy changes.

1.       Fink, T.R. and Crothers, D.M. (1972) Free energy of imperfect nucleic acid helices,  I.  The bulge defect. J. Mol. Biol., 66, 1-12.
2.       Nelson, J.W., Martin, F.H. and Tinoco, I., Jr. (1981) DNA and RNA oligomer thermodynamics: the effect of mismatched bases on double-helix stability. Biopolymers, 20, 2509-2531.
3.       Freier, S.M., Burger, B.J., Alkema, D., Neilson, T. and Turner, D.H. (1983) Effects of 3' dangling end stacking on the stability of GGCC and CCGG double helices. Biochemistry, 22, 6198-6206.
4.       Petersheim, M. and Turner, D.H. (1983) Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry, 22, 256-263.
5.       Freier, S.M., Alkema, D., Sinclair, A., Neilson, T. and Turner, D.H. (1985) Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes. Biochemistry, 24, 4533-4539.
6.       Freier, S.M., Sinclair, A., Neilson, T. and Turner, D.H. (1985) Improved free energies for G-C base-pairs. J. Mol. Biol., 185, 645-647.
7.       Hickey, D.R. and Turner, D.H. (1985) Solvent effects on the stability of A7U7p. Biochemistry, 24, 2086-2094.
8.       Freier, S.M., Kierzek, R., Caruthers, M.H., Neilson, T. and Turner, D.H. (1986) Free energy contributions of G.U and other terminal mismatches to helix stability. Biochemistry, 25, 3209-3223.
9.       Freier, S.M., Kierzek, R., Jaeger, J.A., Sugimoto, N., Caruthers, M.H., Neilson, T. and Turner, D.H. (1986) Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. USA., 83, 9373-9377.
10.     Freier, S.M., Sugimoto, N., Sinclair, A., Alkema, D., Neilson, T., Kierzek, R., Caruthers, M.H. and Turner, D.H. (1986) Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: an empirical estimate of the energetics of hydrogen bonds in nucleic acids. Biochemistry, 25, 3214-3219.
11.     Kierzek, R., Caruthers, M.H., Longfellow, C.E., Swinton, D., Turner, D.H. and Freier, S.M. (1986) Polymer-supported synthesis and its application to test the nearest-neighbor model for duplex stability. Biochemistry, 25, 7840-7846.
12.     Sugimoto, N., Kierzek, R., Freier, S.M. and Turner, D.H. (1986) Energetics of internal GU mismatches in ribooligonucleotide helixes. Biochemistry, 25, 5755-5759.
13.     Sugimoto, N., Kierzek, R. and Turner, D.H. (1987) Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid. Biochemistry, 26, 4554-4558.
14.     Groebe, D.R. and Uhlenbeck, O.C. (1988) Characterization of RNA hairpin loop stability. Nucleic Acids Res., 16, 11725-11735.
15.     Groebe, D.R. and Uhlenbeck, O.C. (1989) Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide. Biochemistry, 28, 742-747.
16.     Longfellow, C.E., Kierzek, R. and Turner, D.H. (1990) Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides. Biochemistry, 29, 278-285.
17.     Antao, V.P., Lai, S.Y. and Tinoco, I., Jr. (1991) A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res., 19, 5901-5905.
18.     Hall, K.B. and McLaughlin, L.W. (1991) Thermodynamic and structural properties of pentamer DNA.DNA, RNA.RNA, and DNA.RNA duplexes of identical sequence. Biochemistry, 30, 10606-10613.
19.     He, L., Kierzek, R., SantaLucia, J., Jr., Walter, A.E. and Turner, D.H. (1991) Nearest-neighbor parameters for G.U mismatches. Biochemistry, 30, 11124-11132.
20.     Peritz, A.E., Kierzek, R., Sugimoto, N. and Turner, D.H. (1991) Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than asymmetric loops. Biochemistry, 30, 6428-6436.
21.     SantaLucia, J., Jr., Kierzek, R. and Turner, D.H. (1991) Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops. J. Am. Chem. Soc., 113, 4313-4322.
22.     SantaLucia, J., Jr., Kierzek, R. and Turner, D.H. (1991) Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: evidence for stable hydrogen-bonded U.U and C.C+ pairs. Biochemistry, 30, 8242-8251.
23.     Antao, V.P. and Tinoco, I., Jr. (1992) Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Res., 20, 819-824.
24.     Serra, M.J., Lyttle, M.H., Axenson, T.J., Schadt, C.A. and Turner, D.H. (1993) RNA hairpin loop stability depends on closing pair. Nucleic Acids Res., 21, 3845-3849.
25.     Serra, M.J., Axenson, T.J. and Turner, D.H. (1994) A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides. Biochemistry, 33, 14289-14296.
26.     Walter, A.E., Turner, D.H., Kim, J., Lyttle, M.H., Müller, P., Mathews, D.H. and Zuker, M. (1994) Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl. Acad. Sci. USA., 91, 9218-9222.
27.     Walter, A.E., Wu, M. and Turner, D.H. (1994) The stability and structure of tandem GA mismatches in RNA depend on closing base pairs. Biochemistry, 33, 11349-11354.
28.     Wu, M., McDowell, J.A. and Turner, D.H. (1995) A periodic table of symmetric tandem mismatches in RNA. Biochemistry, 34, 3204-3211.
29.     Kim, J., Walter, A.E. and Turner, D.H. (1996) Thermodynamics of coaxially stacked helices with GA and CC mismatches. Biochemistry, 35, 13753-13761.
30.     Laing, L.G. and Hall, K.B. (1996) A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data. Biochemistry, 35, 13586-13596.
31.     McDowell, J.A. and Turner, D.H. (1996) Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: Solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing. Biochemistry, 35, 14077-14089.
32.     Schroeder, S., Kim, J. and Turner, D.H. (1996) G.A and U.U mismatches can stabilize RNA internal loops of three nucleotides. Biochemistry, 35, 16105-16109.
33.     McDowell, J.A., He, L., Chen, X. and Turner, D.H. (1997) Investigation of the structural basis for thermodynamic stabilities of tandem GU wobble pairs: NMR structures of (rGGAGUUCC)2 and (rGGAUGUCC)2. Biochemistry, 36, 8030-8038.
34.     Serra, M.J., Barnes, T.W., Betschart, K., Gutierrez, M.J., Sprouse, K.J., Riley, C.K., Stewart, L. and Temel, R.E. (1997) Improved parameters for the prediction of RNA hairpin stability. Biochemistry, 36, 4844-4851.
35.     Xia, T., McDowell, J.A. and Turner, D.H. (1997) Thermodynamics of nonsymmetric tandem mismatches adjacent to G.C base pairs in RNA. Biochemistry, 36, 12486-12487.
36.     Giese, M.R., Betschart, K., Dale, T., Riley, C.K., Rowan, C., Sprouse, K.J. and Serra, M.J. (1998) Stability of RNA hairpins closed by wobble base pairs. Biochemistry, 37, 1094-1100.
37.     Xia, T., SantaLucia, J., Jr., Burkard, M.E., Kierzek, R., Schroeder, S.J., Jiao, X., Cox, C. and Turner, D.H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick pairs. Biochemistry, 37, 14719-14735.
38.     Kierzek, R., Burkard, M. and Turner, D. (1999) Thermodynamics of single mismatches in RNA duplexes. Biochemistry, 38, 14214-14223.
39.     Shu, Z. and Bevilacqua, P.C. (1999) Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library. Biochemistry, 38, 15369-15379.
40.     Dale, T., Smith, R. and Serra, M. (2000) A test of the model to predict unusually stable RNA hairpin loop stability. RNA, 6, 608-615.
41.     Schroeder, S.J. and Turner, D.H. (2000) Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA. Biochemistry, 39, 9257-9274.
42.     Burkard, M.E., Xia, T. and Turner, D.H. (2001) Thermodynamics of RNA internal loops with a guanosine-guanosine pair adjacent to another noncanonical pair. Biochemistry, 40, 2478-2483.
43.     Diamond, J.M., Turner, D.H. and Mathews, D.H. (2001) Thermodynamics of three-way multibranch loops in RNA. Biochemistry, 40, 6971-6981.
44.     Schroeder, S.J. and Turner, D.H. (2001) Thermodynamic stabilities of internal loops with GU closing pairs in RNA. Biochemistry, 40, 11509-11517.
45.     Mathews, D.H. and Turner, D.H. (2002) Experimentally derived nearest neighbor parameters for the stability of RNA three- and four-way multibranch loops. Biochemistry, 41, 869-880.
46.     Proctor, D.J., Schaak, J.E., Bevilacqua, J.M., Falzone, C.J. and Bevilacqua, P.C. (2002) Isolation and characterization of stable tetraloops with the motif YNMG that participates in tertiary interactions. Biochemistry, 41, 12062-12075.
47.     Znosko, B.M., Silvestri, S.B., Volkman, H., Boswell, B. and Serra, M.J. (2002) Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges. Biochemistry, 41, 10406-10417.
48.     Schroeder, S.J., Fountain, M.A., Kennedy, S.D., Lukavsky, P.J., Puglisi, J.D., Krugh, T.R. and Turner, D.H. (2003) Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron. Biochemistry, 42, 14184-14196.

 

The following is a set of references to recent optical melting experiments on RNA that have not yet been used to revise the RNA nearest neighbor parameters:

1.       Vecenie, C.J. and Serra, M.J. (2004) Stability of RNA hairpin loops closed by AU base pairs. Biochemistry, 43, 11813-11817.

2.       Chen, G., Znosko, B.M., Kennedy, S.D., Krugh, T.R. and Turner, D.H. (2005) Solution structure of an RNA internal loop with three consecutive sheared GA pairs. Biochemistry, 44, 2845-2856.

3.       O'Toole, A.S., Miller, S. and Serra, M.J. (2005) Stability of 3' double nucleotide overhangs that model the 3' ends of siRNA. RNA, 11, 512-516.

4.       Chen, G. and Turner, D.H. (2006) Consecutive GA pairs stabilize medium size RNA internal loops. Biochemistry, 45, 4025-4043.

5.       O'Toole, A.S., Miller, S., Haines, N., Zink, M.C. and Serra, M.J. (2006) Comprehensive thermodynamic analysis of 3' double-nucleotide overhangs neighboring Watson-Crick terminal base pairs. Nucleic Acids Res., 34, 3338-3344.

6.       Shankar, N., Kennedy, S.D., Chen, G., Krugh, T.R. and Turner, D.H. (2006) The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits. Biochemistry, 45, 11776-11789.

7.       Vecenie, C.J., Morrow, C.V., Zyra, A. and Serra, M.J. (2006) Sequence dependence of the stability of RNA hairpin molecules with six nucleotide loops. Biochemistry, 45, 1400-1407.

8.       Badhwar, J., Karri, S., Cass, C.K., Wunderlich, E.L. and Znosko, B.M. (2007) Thermodynamic characterization of RNA duplexes containing naturally occurring 1 x 2 nucleotide internal loops. Biochemistry, 46, 14715-14724.

9.       Blose, J.M., Manni, M.L., Klapec, K.A., Stranger-Jones, Y., Zyra, A.C., Sim, V., Griffith, C.A., Long, J.D. and Serra, M.J. (2007) Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops. Biochemistry, 46, 15123-15135.

10.     Davis, A.R. and Znosko, B.M. (2007) Thermodynamic characterization of single mismatches found in naturally occurring RNA. Biochemistry, 46, 13425-13436.

11.     Shankar, N., Xia, T., Kennedy, S.D., Krugh, T.R., Mathews, D.H. and Turner, D.H. (2007) NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA. Biochemistry, 46, 12665-12678.

12.     Siegfried, N.A., Metzger, S.L. and Bevilacqua, P.C. (2007) Folding cooperativity in RNA and DNA is dependent on position in the helix. Biochemistry, 46, 172-181.

13.     Tolbert, B.S., Kennedy, S.D., Schroeder, S.J., Krugh, T.R. and Turner, D.H. (2007) NMR structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: probing the structural features that shape the thermodynamic stability of GA pairs. Biochemistry, 46, 1511-1522.

14.     Christiansen, M.E. and Znosko, B.M. (2008) Thermodynamic characterization of the complete set of sequence symmetric tandem mismatches in RNA and an improved model for predicting the free energy contribution of sequence asymmetric tandem mismatches. Biochemistry, 47, 4329-4336.

15.     Clanton-Arrowood, K., McGurk, J. and Schroeder, S.J. (2008) 3' terminal nucleotides determine thermodynamic stabilities of mismatches at the ends of RNA helices. Biochemistry, 47, 13418-13427.

16.     Davis, A.R. and Znosko, B.M. (2008) Thermodynamic characterization of naturally occurring RNA single mismatches with G-U nearest neighbors. Biochemistry, 47, 10178-10187.

17.     Miller, S., Jones, L.E., Giovannitti, K., Piper, D. and Serra, M.J. (2008) Thermodynamic analysis of 5' and 3' single- and 3' double-nucleotide overhangs neighboring wobble terminal base pairs. Nucleic Acids Res., 36, 5652-5659.

18.     Blose, J.M., Proctor, D.J., Veeraraghavan, N., Misra, V.K. and Bevilacqua, P.C. (2009) Contribution of the closing base pair to exceptional stability in RNA tetraloops: roles for molecular mimicry and electrostatic factors. J. Am. Chem. Soc., 131, 8474-8484.

19.     Chen, G., Kennedy, S.D. and Turner, D.H. (2009) A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops. Biochemistry, 48, 5738-5752.

20.     Christiansen, M.E. and Znosko, B.M. (2009) Thermodynamic characterization of tandem mismatches found in naturally occurring RNA. Nucleic Acids Res., 37, 4696-4706.

 

Page Revised 8/14/2009